Linking like with like: optimising connectivity between environmentally-similar habitats

Habitat fragmentation is one of the greatest threats to biodiversity. To minimise the effect of fragmentation on biodiversity, connectivity between otherwise isolated habitats should be promoted. However, the identification of linkages favouring connectivity is not trivial. Firstly, they compete with other land uses, so they need to be cost-efficient. Secondly, linkages for one species might be barriers for others, so they should effectively account for distinct mobility requirements. Thirdly, detailed information on the auto-ecology of most of the species is lacking, so linkages need being defined based on surrogates. In order to address these challenges we develop a framework that (a) identifies environmentally-similar habitats; (b) identifies environmental barriers (i.e., regions with a very distinct environment from the areas to be linked), and; (c) determines cost-efficient linkages between environmentally-similar habitats, free from environmental barriers. The assumption is that species with similar ecological requirements occupy the same environments, so environmental similarity provides a rationale for the identification of the areas that need to be linked. A variant of the classical minimum Steiner tree problem in graphs is used to address c). We present a heuristic for this problem that is capable of handling large datasets. To illustrate the framework we identify linkages between environmentally-similar protected areas in the Iberian Peninsula. The Natura 2000 network is used as a positive ‘attractor’ of links while the human footprint is used as ‘repellent’ of links.Wecompare the outcomes of our approach with cost-efficient networks linking protected areas that disregard the effect of environmental barriers. As expected, the latter achieved a smaller area covered with linkages, but with barriers that can significantly reduce the permeability of the landscape for the dispersal of some species

Generation of a large volume of clinically relevant nanometre-sized ultra-high-molecular-weight polyethylene wear particles for cell culture studies.

It has recently been shown that the wear of ultra-high-molecular-weight polyethylene in hip and knee prostheses leads to the generation of nanometre-sized particles, in addition to micron-sized particles. The biological activity of nanometre-sized ultra-high-molecular-weight polyethylene wear particles has not, however, previously been studied due to difficulties in generating sufficient volumes of nanometre-sized ultra-high-molecular-weight polyethylene wear particles suitable for cell culture studies. In this study, wear simulation methods were investigated to generate a large volume of endotoxin-free clinically relevant nanometre-sized ultra-high-molecular-weight polyethylene wear particles. Both single-station and six-station multidirectional pin-on-plate wear simulators were used to generate ultra-high-molecular-weight polyethylene wear particles under sterile and non-sterile conditions. Microbial contamination and endotoxin levels in the lubricants were determined. The results indicated that microbial contamination was absent and endotoxin levels were low and within acceptable limits for the pharmaceutical industry, when a six-station pin-on-plate wear simulator was used to generate ultra-high-molecular-weight polyethylene wear particles in a non-sterile environment. Different pore-sized polycarbonate filters were investigated to isolate nanometre-sized ultra-high-molecular-weight polyethylene wear particles from the wear test lubricants. The use of the filter sequence of 10, 1, 0.1, 0.1 and 0.015 µm pore sizes allowed successful isolation of ultra-high-molecular-weight polyethylene wear particles with a size range of < 100 nm, which was suitable for cell culture studies

Quantitative Analysis of Immune Response and Erythropoiesis during Rodent Malarial Infection

Malarial infection is associated with complex immune and erythropoietic responses in the host. A quantitative understanding of these processes is essential to help inform malaria therapy and for the design of effective vaccines. In this study, we use a statistical model-fitting approach to investigate the immune and erythropoietic responses in Plasmodium chabaudi infections of mice. Three mouse phenotypes (wildtype, T-cell-deficient nude mice, and nude mice reconstituted with T-cells taken from wildtype mice) were infected with one of two parasite clones (AS or AJ). Under a Bayesian framework, we use an adaptive population-based Markov chain Monte Carlo method and fit a set of dynamical models to observed data on parasite and red blood cell (RBC) densities. Model fits are compared using Bayes' factors and parameter estimates obtained. We consider three independent immune mechanisms: clearance of parasitised RBCs (pRBC), clearance of unparasitised RBCs (uRBC), and clearance of parasites that burst from RBCs (merozoites). Our results suggest that the immune response of wildtype mice is associated with less destruction of uRBCs, compared to the immune response of nude mice. There is a greater degree of synchronisation between pRBC and uRBC clearance than between either mechanism and merozoite clearance. In all three mouse phenotypes, control of the peak of parasite density is associated with pRBC clearance. In wildtype mice and AS-infected nude mice, control of the peak is also associated with uRBC clearance. Our results suggest that uRBC clearance, rather than RBC infection, is the major determinant of RBC dynamics from approximately day 12 post-innoculation. During the first 2–3 weeks of blood-stage infection, immune-mediated clearance of pRBCs and uRBCs appears to have a much stronger effect than immune-mediated merozoite clearance. Upregulation of erythropoiesis is dependent on mouse phenotype and is greater in wildtype and reconstitited mice. Our study highlights the informative power of statistically rigorous model-fitting techniques in elucidating biological systems

Long-Distance Delivery of Bacterial Virulence Factors by Pseudomonas aeruginosa Outer Membrane Vesicles

Bacteria use a variety of secreted virulence factors to manipulate host cells, thereby causing significant morbidity and mortality. We report a mechanism for the long-distance delivery of multiple bacterial virulence factors, simultaneously and directly into the host cell cytoplasm, thus obviating the need for direct interaction of the pathogen with the host cell to cause cytotoxicity. We show that outer membrane–derived vesicles (OMV) secreted by the opportunistic human pathogen Pseudomonas aeruginosa deliver multiple virulence factors, including β-lactamase, alkaline phosphatase, hemolytic phospholipase C, and Cif, directly into the host cytoplasm via fusion of OMV with lipid rafts in the host plasma membrane. These virulence factors enter the cytoplasm of the host cell via N-WASP–mediated actin trafficking, where they rapidly distribute to specific subcellular locations to affect host cell biology. We propose that secreted virulence factors are not released individually as naked proteins into the surrounding milieu where they may randomly contact the surface of the host cell, but instead bacterial derived OMV deliver multiple virulence factors simultaneously and directly into the host cell cytoplasm in a coordinated manner

Relationship between early development of spelling and reading

The research reported in this thesis examined the relationship between beginning spelling and reading. More specifically, it focussed on the relationship between the development of early reading and spelling in a context where the approach to early reading instruction includes systematic phonological awareness and decoding instruction. A critical assumption made by proponents of developmental early literacy models is that transfer of skills and knowledge from reading to spelling will occur spontaneously and without formal instruction (Frith, 1980). By contrast instruction-centred approaches make the assumption that there are critical pre-requisite skills that can and should be taught explicitly (Carnine, Silbert & Kameenui, 1997). The difference between these approaches is highlighted in the treatment of invented spelling, a popular activity in Western Australian junior primary classes. A series of studies was undertaken to examine the effect on invented and standard spelling performance of teaching Year 1 children phonological awareness and the strategy of sounding out words. Data were gathered from a range of settings using different research tools. The relationship between phonological awareness and beginning reading and spelling performance was explored initially through a single case study. A post-hoc study was then undertaken with a cohort of students who had received systematic decoding instruction to examine whether proficiency in the decoding of nonwords was related to spelling performance. This permitted an analysis of common sub-skills of decoding and encoding. In the main study the effect on different aspects of reading and spelling performance of using Let\u27s Decode, an approach that includes explicit phonological awareness and systematic decoding instruction, was investigated. In addition, an analysis was made of whether students who received explicit instruction in skills known to contribute to beginning reading and spelling produced superior invented spelling samples. A qualitative analysis was made of the. pre and post invented spelling tests of two pairs of students from the control and intervention groups matched on invented spelling and phonological awareness skills at the beginning of the year, and re tested at the end of Year 1. The final research question involved a single-subject research design to examine the effect of explicit instruction in isolating phonemes in words and prompts to \u27listen for sounds\u27 prior to, and during, the process of spelling words. The single case study revealed a child who was regarded as a competent speller and reader but who could only read words in a familiar context and who had developed a strategy for spelling words based on copying an adult model. This was interpreted as evidence supporting the need for phonological awareness instruction as a pre-requisite for spelling. The post-hoc analysis of a class of students who had received systematic decoding instruction showed that no student classified as a \u27good decoder\u27 could also be classified as a \u27poor speller\u27. This result was considered evidence of a strong link between the phonological knowledge that is required to decode and the role of alphabetic knowledge in spelling. The main study revealed phonological awareness and systematic decoding instruction was associated with superior invented and conventional spelling and reading performance on all reading and spelling measures. Of particular importance was the finding that students who commenced the study with very weak phonological awareness and who subsequently received systematic phonological and decoding instruction showed greater gains in invented spelling than matched students in the control condition. The single subject design showed the effectiveness of phonological awareness individualised instruction on invented spelling for weak students from both intervention and control conditions. It was concluded that the ability to invent spelling is improved when students receive explicit instruction in phonological awareness and systematic decoding but that some students, namely those with persistent weakness in phonological awareness, also require explicit prompts to apply their alphabetic knowledge to spelling words. The implications for instruction of these findings are discussed

High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution

Olfactory receptors (ORs), which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected by the relatively small repertoire size and the high fraction (∼55%) of human pseudogenes. Since several recent low-resolution surveys suggested that OR genomic loci are frequently affected by copy-number variants (CNVs), we hypothesized that CNVs may play an important role in the evolution of the human olfactory repertoire. We used high-resolution oligonucleotide tiling microarrays to detect CNVs across 851 OR gene and pseudogene loci. Examining genomic DNA from 25 individuals with ancestry from three populations, we identified 93 OR gene loci and 151 pseudogene loci affected by CNVs, generating a mosaic of OR dosages across persons. Our data suggest that ∼50% of the CNVs involve more than one OR, with the largest CNV spanning 11 loci. In contrast to earlier reports, we observe that CNVs are more frequent among OR pseudogenes than among intact genes, presumably due to both selective constraints and CNV formation biases. Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee. Interestingly, among the latter we observed an enrichment in CNV losses over gains, a finding potentially related to the known diminution of the human OR repertoire. Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs. Importantly, these experiments allowed us to uncover nine common deletion alleles that affect 15 OR genes and five pseudogenes. Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content. Furthermore, these deletion alleles may be used in future genetic association studies of olfactory inter-individual differences

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

A Rapid and Sensitive Method for Measuring NAcetylglucosaminidase Activity in Cultured Cells

A rapid and sensitive method to quantitatively assess N-acetylglucosaminidase (NAG) activity in cultured cells is highly desirable for both basic research and clinical studies. NAG activity is deficient in cells from patients with Mucopolysaccharidosis type IIIB (MPS IIIB) due to mutations in NAGLU, the gene that encodes NAG. Currently available techniques for measuring NAG activity in patient-derived cell lines include chromogenic and fluorogenic assays and provide a biochemical method for the diagnosis of MPS IIIB. However, standard protocols require large amounts of cells, cell disruption by sonication or freeze-thawing, and normalization to the cellular protein content, resulting in an error-prone procedure that is material- and time-consuming and that produces highly variable results. Here we report a new procedure for measuring NAG activity in cultured cells. This procedure is based on the use of the fluorogenic NAG substrate, 4- Methylumbelliferyl-2-acetamido-2-deoxy-alpha-D-glucopyranoside (MUG), in a one-step cell assay that does not require cell disruption or post-assay normalization and that employs a low number of cells in 96-well plate format. We show that the NAG one-step cell assay greatly discriminates between wild-type and MPS IIIB patient-derived fibroblasts, thus providing a rapid method for the detection of deficiencies in NAG activity. We also show that the assay is sensitive to changes in NAG activity due to increases in NAGLU expression achieved by either overexpressing the transcription factor EB (TFEB), a master regulator of lysosomal function, or by inducing TFEB activation chemically. Because of its small format, rapidity, sensitivity and reproducibility, the NAG one-step cell assay is suitable for multiple procedures, including the high-throughput screening of chemical libraries to identify modulators of NAG expression, folding and activity, and the investigation of candidate molecules and constructs for applications in enzyme replacement therapy, gene therapy, and combination therapies

Expression of matrix metalloproteinase-1 (MMP-1) in Wistar rat's intervertebral disc after experimentally induced scoliotic deformity

<p>Abstract</p> <p>Introduction</p> <p>A scoliotic deformity on intervertebral discs may accelerate degeneration at a molecular level with the production of metalloproteinases (MMPs). In the present experimental study we evaluated the presence of MMP-1 immunohistochemically after application of asymmetric forces in a rat intervertebral disc and the impact of the degree of the deformity on MMP-1 expression.</p> <p>Material-Method</p> <p>Thirty female Wistar rats (aged 2 months old, weighted 200 ± 10 grams) were used. All animals were age, weight and height matched. A mini Ilizarov external fixator was applied at the base of a rat tail under anaesthesia in order to create a scoliotic deformity of the intervertebral disc between the 9^thand 10^thvertebrae. Rats were divided into three groups according to the degree of the deformity. In group I, the deformity was 10°, in group II 30° and in group III 50°. The rats were killed 35 days after surgery. The discs were removed along with the neighbouring vertebral bodies, prepared histologically and stained immunohistochemically. Immunopositivity of disc's cells for MMP-1 was determined using a semi-quantitative scored system.</p> <p>Results</p> <p>MMP-1 immunopositivity was detected in disc cells of annulus fibrosus of all intervertebral disc specimens examined. The percentage of MMP-1 positive disc cells in annulus fibrosus in group I, II and III were 20%, 43% and 75%, respectively. MMP-1 positivity was significantly correlated with the degree of the deformity (p < 0,001). An increase of chondrocyte-like disc cells was observed in the outer annulus fibrosus and at the margin of the intervertebral disc adjacent to the vertebral end plates. The difference in the proportion of MMP-1 positive disc cells between the convex and the concave side was statistically not significant in group I (p = 0,6), in group II this difference was statistically significant (p < 0,01). In group III the concave side showed a remarkable reduction in the number of disc's cells and a severe degeneration of matrix microstructure.</p> <p>Conclusion</p> <p>The present study showed that an experimentally induced scoliotic deformity on a rat tail intervertebral disc results in over-expression of MMP-1, which is dependent on the degree of the deformity and follows a dissimilar distribution between the convex and the concave side.</p